[Genbank-bb] GenBank Release 193.0 Available : December 14 2012

Cavanaugh, Mark (NIH/NLM/NCBI) [E] via genbankb%40net.bio.net (by cavanaug from ncbi.nlm.nih.gov)
Fri Dec 14 18:07:33 EST 2012


Greetings GenBank Users,

  GenBank Release 193.0 is now available via FTP from the
National Center for Biotechnology Information (NCBI):

  Ftp Site           Directory   Contents
  ----------------   ---------   ---------------------------------------
  ftp.ncbi.nih.gov   genbank     GenBank Release 193.0 flatfiles
                     ncbi-asn1   ASN.1 data used to create Release 193.0

  Close-of-data for GenBank 193.0 occurred on 12/12/2012. Uncompressed,
the Release 193.0 flatfiles require roughly 579 GB (sequence files only)
or 624 GB (including the 'short directory', 'index' and the *.txt files).
The ASN.1 data require approximately 474 GB.

Recent statistics for non-WGS, non-CON sequences:

  Release  Date      Base Pairs    Entries

  192      Oct 2012  145430961262  157889737
  193      Dec 2012  148390863904  161140325

Recent statistics for WGS sequences:

  Release  Date      Base Pairs    Entries

  192    Oct 2012  333881846451   86480509
  193    Dec 2012  356002922838   92767765

  During the 65 days between the close dates for GenBank Releases 192.0
and 193.0, the non-WGS/non-CON portion of GenBank grew by 2,959,902,642
basepairs and by 3,250,588 sequence records. During that same period,
830,113 records were updated. An average of 62,780 non-WGS/non-CON
records were added and/or updated per day.

  Between releases 192.0 and 193.0, the WGS component of GenBank grew by
22,121,076,387 basepairs and by 6,287,256 sequence records.

  For additional release information, see the README files in either of
the directories mentioned above, and the release notes (gbrel.txt) in
the genbank directory. Sections 1.3 and 1.4 of the release notes
(Changes in Release 193.0 and Upcoming Changes) have been appended
below for your convenience.

~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~
                    ** Important Note **

   New data products intended to replace the legacy 'index' files that
   accompany the sequence-data files of GenBank releases are being
   prepared, and will soon be made available at the NCBI FTP site.
   We will post to the GenBank newsgroup when they have been installed.
   See Section 1.3.4 of the release notes for further details about
   this change. We welcome your feedback about this change.
~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~-~

  Release 193.0 data, and subsequent updates, are available now via
NCBI's Entrez and Blast services.

  As a general guideline, we suggest first transferring the GenBank
release notes (gbrel.txt) whenever a release is being obtained. Check
to make sure that the date and release number in the header of the
release notes are current (eg: December 15 2012, 193.0). If they are
not, interrupt the remaining transfers and then request assistance from
the NCBI Service Desk.

  A comprehensive check of the headers of all release files after your
transfers are complete is also suggested. Here's how one might go about
this on a Unix or Linux platform, using csh/tcsh :

        set files = `ls gb*.*`
        foreach i ($files)
                head -10 $i | grep Release
        end

Or, if the files are compressed, perhaps:

        gzcat $i | head -10 | grep Release

  If you encounter problems while ftp'ing or uncompressing Release
193.0, please send email outlining your difficulties to:

        info from ncbi.nlm.nih.gov

Mark Cavanaugh, Michael Kimelman, Ilya Dondoshansky, Sergey Zhdanov
GenBank
NCBI/NLM/NIH/HHS


1.3 Important Changes in Release 193.0

1.3.1 Organizational changes

The total number of sequence data files increased by 45 with this release:

  - the BCT division is now composed of  94 files (+3)
  - the CON division is now composed of 179 files (+3)
  - the EST division is now composed of 469 files (+3)
  - the GSS division is now composed of 266 files (+6)
  - the PAT division is now composed of 186 files (+4)
  - the PLN division is now composed of  60 files (+1)
  - the ROD division is now composed of  30 files (+1)
  - the TSA division is now composed of 133 files (+21)
  - the VRL division is now composed of  24 files (+2)
  - the VRT division is now composed of  28 files (+1)

The total number of 'index' files increased by 4 with this release:

  - the AUT (author name) index is now composed of 106 files (+4)

1.3.2 Correction of /frequency change announced for GenBank 192.0

  In Section 1.3.5 of the GenBank 192.0 Release Notes (gbrel.txt),
we incorrectly stated that:

  "So as of the October 2012 GenBank release, the /frequency qualifier has
been deprecated. Existing values for the qualifier are now presented via the
/note qualifier of source features, and GenBank submission tools are being
updated to cease support of /frequency."

  However, this *only* applies to /frequency qualifiers on source features.
Obviously, the /frequency qualifier provides information that is very
important for any variation feature, and it will continue to be supported
in that context. Only /frequency for source features has been deprecated.
Our apologies for mis-stating the nature of the /frequency change.

1.3.3 Correction of the format for /anticodon qualifiers

  Subsequent to the generation of the GenBank Release 192.0 data files,
it was discovered that the new "seq" field for the /anticodon qualifier
was improperly formatted:

a) The sequence of the anticodon was presented in the RNA alphabet
   rather than the DNA alphabet.

b) The sequence of the anticodon was presented in uppercase letters
   rather than lowercase letters.

Here is an example that illustrates these problems:

LOCUS       CP003206             2535346 bp    DNA     circular BCT 05-JUN-2012
DEFINITION  Corynebacterium diphtheriae 31A, complete genome.
ACCESSION   CP003206
VERSION     CP003206.1  GI:371577018
DBLINK      BioProject: PRJNA42399
....
     tRNA            complement(2017207..2017282)
                     /locus_tag="CD31A_t050"
                     /product="tRNA-Thr"
                     /anticodon=(pos:complement(2017247..2017249),aa:Thr,
                     seq:UGU)

The proper format for the qualifier is:

                     /anticodon=(pos:complement(2017247..2017249),aa:Thr,
                     seq:tgt)

An update of the flatfile generator software was deployed on October 24 2012
which corrected this problem, for records appearing in GenBank Incremental
Update products. And now, this error is also corrected for all of the
anticodon qualifers that appear in the December 2012 GenBank 193.0 data files.
Our apologies for any inconvenience that this may have caused for our users.

1.3.4 Release Catalog data files to replace old "index" files

  As described in Section 1.3.5, the legacy "index" files that accompany
the sequence data files of GenBank releases have limited utility. For the
past six years we have provided only partial support for them, and have
warned that we plan to cease support entirely. As of GenBank 193.0 we are
introducing experimental "release catalog" products that will eventually
replace the old "index" files. We expect to make the release catalog(s)
and other supplemental files available shortly after Release 193.0 is
installed at the NCBI FTP site.

  Every GenBank sequence record will be represented in the catalog by a
10-field, TAB-delimited row of data. The data fields are:

	Accession Number
	Accession.Version
	NCBI GI Identifier
	Molecule Type (dna, rna, mrna, etc)
	Sequence Length
	Organism Name
	NCBI Taxonomy Database Identifier
	Division Code
	BioProject Accession Number
	BioSample Accession Number

When a value does not exist for one of these fields, the field in the catalog
will be empty (eg, two sequential TAB characters can be present, with
nothing between them). Here is an example of the catalog data for CP003933:

CP003933	CP003933.1	429549985	dna	3618794	Sinorhizobium meliloti GR4	1235461	BCT	PRJNA175860 

It is our hope that the release catalog will be more useful than the current
accession number index files (gbacc*.idx).

  The author-name (gbaut*.idx) and keyword (gbkey*.idx) and secondary-accession
(gbsec*.idx) index files will be discontinued without replacements.

  However, new "PMID List" and "Gene List" TAB-delimited files will accompany
the release catalog. The format of the PubMed Identifier List is:

Accession1	Accession1.Version	PMID-1,PMID-2,PMID-3,.....
Accession2	Accession2.Version	PMID-1,PMID-2,PMID-3,.....
....

And the format of the Gene List is:

Accession1	Accession1.Version	Gene-Symbol-1	Locus-Tag-1
Accession1	Accession1.Version	Gene-Symbol-2	Locus-Tag-2
Accession1	Accession1.Version	Gene-Symbol-3	Locus-Tag-3
Accession2	Accession2.Version	Gene-Symbol-1	Locus-Tag-1
Accession2	Accession2.Version	Gene-Symbol-2	Locus-Tag-2
Accession2	Accession2.Version	Gene-Symbol-3	Locus-Tag-3
....

Note that either Gene Symbol or Locus Tag could be null for any given
gene.

  For now, we plan to provide the release catalog and accompanying lists
via files that are specific to EST, GSS, and non-EST/GSS (everything else).
And, initially, the catalogs and lists will not include the contig 
sequence records for WGS projects. The new files will be made available
in a new sub-directory of the GenBank FTP area:

	 genbank/catalog

And their names will be:

    	  gb193.est.catalog.txt.gz
    	  gb193.gss.catalog.txt.gz
    	  gb193.other.catalog.txt.gz

	  gb193.est.pmid_list.txt.gz
	  gb193.gss.pmid_list.txt.gz
	  gb193.other.pmid_list.txt.gz

	  gb193.est.gene_list.txt.gz
	  gb193.gss.gene_list.txt.gz
	  gb193.other.gene_list.txt.gz

  Our goal is to provide companion products for the release files which will
be of help for large-scale consumers of GenBank data. To that end, if you
have ideas for how to make the release catalog more useful, or have
suggestions for additional companion files like the PMID and Gene lists,
please let us know by contacting the NCBI Help Desk : info from ncbi.nlm.nih.gov .

  Be aware that these new products are still in the experimental stage.
If you encounter problems with their content, we would appreciate your
feedback (again, via the NCBI Help Desk).

1.3.5 Changes in the content of index files

  As described in the GB 153 release notes, the 'index' files which accompany
GenBank releases (see Section 3.3) are considered to be a legacy data product by
NCBI, generated mostly for historical reasons. FTP statistics from January 2005
seemed to support this: the index files were transferred only half as frequently as
the files of sequence records. The inherent inefficiencies of the index file
format also lead us to suspect that they have little serious use by the user
community, particularly for EST and GSS records.

  The software that generated the index file products received little
attention over the years, and finally reached its limitations in
February 2006 (Release 152.0). The required multi-server queries which
obtained and sorted many millions of rows of terms from several different
databases simply outgrew the capacity of the hardware used for GenBank
Release generation.

  Our short-term solution is to cease generating some index-file content
for all EST sequence records, and for GSS sequence records that originate
via direct submission to NCBI.

  The three gbacc*.idx index files continue to reflect the entirety of the
release, including all EST and GSS records, however the file contents are
unsorted.

  These 'solutions' are really just stop-gaps, and we will likely pursue
one of two options:

a) Cease support of the 'index' file products altogether.

b) Provide new products that present some of the most useful data from
   the legacy 'index' files, and cease support for other types of index data.

  If you are a user of the 'index' files associated with GenBank releases, we
encourage you to make your wishes known, either via the GenBank newsgroup,
or via email to NCBI's Service Desk:

   info from ncbi.nlm.nih.gov

  Our apologies for any inconvenience that these changes may cause.

1.3.6 GSS File Header Problem

  GSS sequences at GenBank are maintained in two different systems, depending
on their origin, and the dumps from those systems occur in parallel. Because
the second dump (for example) has no prior knowledge of exactly how many GSS
files will be dumped by the first, it does not know how to number its own
output files.

  There is thus a discrepancy between the filenames and file headers for 111
of the GSS flatfiles in Release 193.0. Consider gbgss156.seq :

GBGSS1.SEQ          Genetic Sequence Data Bank
                        December 15 2012

                NCBI-GenBank Flat File Release 193.0

                           GSS Sequences (Part 1)

   87073 loci,    63907368 bases, from    87073 reported sequences

  Here, the filename and part number in the header is "1", though the file
has been renamed as "156" based on the number of files dumped from the other
system.  We hope to resolve this discrepancy at some point, but the priority
is certainly much lower than many other tasks.

1.4 Upcoming Changes

  No changes impacting the flatfile format are expected between the
December 2012 and February 2013 GenBank releases.






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